Starting phenix.real_space_refine on Fri May 9 13:33:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ggr_40018/05_2025/8ggr_40018.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ggr_40018/05_2025/8ggr_40018.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ggr_40018/05_2025/8ggr_40018.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ggr_40018/05_2025/8ggr_40018.map" model { file = "/net/cci-nas-00/data/ceres_data/8ggr_40018/05_2025/8ggr_40018.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ggr_40018/05_2025/8ggr_40018.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 1434 2.51 5 N 335 2.21 5 O 358 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 2143 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2127 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 7, 'TRANS': 273} Chain breaks: 1 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 90 Chain: "R" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 2.58, per 1000 atoms: 1.20 Number of scatterers: 2143 At special positions: 0 Unit cell: (55.5328, 85.0346, 62.4744, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 16 16.00 O 358 8.00 N 335 7.00 C 1434 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.47 Conformation dependent library (CDL) restraints added in 229.7 milliseconds 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 538 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 0 sheets defined 89.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'R' and resid 32 through 61 removed outlier: 3.779A pdb=" N GLY R 37 " --> pdb=" O VAL R 33 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N MET R 40 " --> pdb=" O MET R 36 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 65 Processing helix chain 'R' and resid 68 through 97 removed outlier: 3.998A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 102 through 137 removed outlier: 3.505A pdb=" N SER R 137 " --> pdb=" O PHE R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 removed outlier: 3.502A pdb=" N LEU R 145 " --> pdb=" O TYR R 141 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 171 removed outlier: 3.508A pdb=" N ALA R 150 " --> pdb=" O THR R 146 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL R 152 " --> pdb=" O ASN R 148 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER R 165 " --> pdb=" O SER R 161 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Proline residue: R 168 - end of helix removed outlier: 3.635A pdb=" N MET R 171 " --> pdb=" O LEU R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 187 Processing helix chain 'R' and resid 196 through 208 Processing helix chain 'R' and resid 208 through 237 Processing helix chain 'R' and resid 270 through 299 removed outlier: 4.078A pdb=" N THR R 274 " --> pdb=" O LYS R 270 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE R 278 " --> pdb=" O THR R 274 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.616A pdb=" N VAL R 292 " --> pdb=" O PRO R 288 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILE R 298 " --> pdb=" O ILE R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 317 removed outlier: 3.810A pdb=" N TYR R 308 " --> pdb=" O ARG R 304 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE R 309 " --> pdb=" O LYS R 305 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 327 removed outlier: 3.652A pdb=" N PHE R 321 " --> pdb=" O VAL R 317 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN R 322 " --> pdb=" O ASN R 318 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 329 through 340 163 hydrogen bonds defined for protein. 486 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.52 Time building geometry restraints manager: 0.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 633 1.35 - 1.46: 570 1.46 - 1.58: 972 1.58 - 1.70: 0 1.70 - 1.81: 23 Bond restraints: 2198 Sorted by residual: bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.450 -0.053 2.00e-02 2.50e+03 6.91e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.572 -0.049 2.00e-02 2.50e+03 5.97e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.565 -0.045 2.00e-02 2.50e+03 5.02e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.438 -0.044 2.00e-02 2.50e+03 4.91e+00 bond pdb=" CAD G1I R 501 " pdb=" OAK G1I R 501 " ideal model delta sigma weight residual 1.353 1.322 0.031 2.00e-02 2.50e+03 2.38e+00 ... (remaining 2193 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 2901 1.12 - 2.24: 82 2.24 - 3.36: 19 3.36 - 4.48: 4 4.48 - 5.60: 7 Bond angle restraints: 3013 Sorted by residual: angle pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " pdb=" CAI G1I R 501 " ideal model delta sigma weight residual 110.89 116.49 -5.60 3.00e+00 1.11e-01 3.49e+00 angle pdb=" CAE G1I R 501 " pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 112.63 118.21 -5.58 3.00e+00 1.11e-01 3.46e+00 angle pdb=" N ILE R 94 " pdb=" CA ILE R 94 " pdb=" CB ILE R 94 " ideal model delta sigma weight residual 110.57 112.94 -2.37 1.28e+00 6.10e-01 3.42e+00 angle pdb=" CB MET R 279 " pdb=" CG MET R 279 " pdb=" SD MET R 279 " ideal model delta sigma weight residual 112.70 117.41 -4.71 3.00e+00 1.11e-01 2.46e+00 angle pdb=" C SER R 207 " pdb=" N PHE R 208 " pdb=" CA PHE R 208 " ideal model delta sigma weight residual 122.46 119.69 2.77 1.80e+00 3.09e-01 2.37e+00 ... (remaining 3008 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.06: 1129 17.06 - 34.12: 105 34.12 - 51.18: 20 51.18 - 68.24: 0 68.24 - 85.30: 3 Dihedral angle restraints: 1257 sinusoidal: 429 harmonic: 828 Sorted by residual: dihedral pdb=" CB CYS R 106 " pdb=" SG CYS R 106 " pdb=" SG CYS R 191 " pdb=" CB CYS R 191 " ideal model delta sinusoidal sigma weight residual -86.00 -171.30 85.30 1 1.00e+01 1.00e-02 8.81e+01 dihedral pdb=" CA TYR R 174 " pdb=" C TYR R 174 " pdb=" N ARG R 175 " pdb=" CA ARG R 175 " ideal model delta harmonic sigma weight residual -180.00 -162.22 -17.78 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA PHE R 208 " pdb=" C PHE R 208 " pdb=" N TYR R 209 " pdb=" CA TYR R 209 " ideal model delta harmonic sigma weight residual 180.00 -163.84 -16.16 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 1254 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 218 0.029 - 0.058: 102 0.058 - 0.087: 36 0.087 - 0.116: 14 0.116 - 0.145: 2 Chirality restraints: 372 Sorted by residual: chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.54 -0.14 2.00e-01 2.50e+01 5.22e-01 chirality pdb=" CA PRO R 138 " pdb=" N PRO R 138 " pdb=" C PRO R 138 " pdb=" CB PRO R 138 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.48e-01 chirality pdb=" CA PRO R 288 " pdb=" N PRO R 288 " pdb=" C PRO R 288 " pdb=" CB PRO R 288 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.98e-01 ... (remaining 369 not shown) Planarity restraints: 359 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 167 " -0.025 5.00e-02 4.00e+02 3.81e-02 2.32e+00 pdb=" N PRO R 168 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO R 168 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO R 168 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 173 " -0.010 2.00e-02 2.50e+03 6.01e-03 9.03e-01 pdb=" CG TRP R 173 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 TRP R 173 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP R 173 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP R 173 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP R 173 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 173 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 173 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 173 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP R 173 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 174 " -0.005 2.00e-02 2.50e+03 6.69e-03 8.96e-01 pdb=" CG TYR R 174 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR R 174 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR R 174 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR R 174 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR R 174 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR R 174 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR R 174 " 0.001 2.00e-02 2.50e+03 ... (remaining 356 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 822 2.89 - 3.39: 2198 3.39 - 3.89: 3321 3.89 - 4.40: 3453 4.40 - 4.90: 6239 Nonbonded interactions: 16033 Sorted by model distance: nonbonded pdb=" OH TYR R 185 " pdb=" O PHE R 194 " model vdw 2.387 3.040 nonbonded pdb=" OD1 ASN R 196 " pdb=" N GLN R 197 " model vdw 2.475 3.120 nonbonded pdb=" OG SER R 120 " pdb=" O HOH R 601 " model vdw 2.519 3.040 nonbonded pdb=" OE1 GLU R 107 " pdb=" OH TYR R 174 " model vdw 2.524 3.040 nonbonded pdb=" O THR R 189 " pdb=" OG1 THR R 189 " model vdw 2.525 3.040 ... (remaining 16028 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.120 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 2199 Z= 0.191 Angle : 0.543 5.602 3015 Z= 0.287 Chirality : 0.040 0.145 372 Planarity : 0.004 0.038 359 Dihedral : 13.102 72.445 716 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.51), residues: 277 helix: 2.21 (0.35), residues: 212 sheet: None (None), residues: 0 loop : -2.00 (0.65), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 173 HIS 0.003 0.001 HIS R 296 PHE 0.014 0.001 PHE R 139 TYR 0.016 0.001 TYR R 174 ARG 0.005 0.001 ARG R 175 Details of bonding type rmsd hydrogen bonds : bond 0.13862 ( 163) hydrogen bonds : angle 5.24854 ( 486) SS BOND : bond 0.00232 ( 1) SS BOND : angle 0.42313 ( 2) covalent geometry : bond 0.00408 ( 2198) covalent geometry : angle 0.54315 ( 3013) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.235 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.1969 time to fit residues: 6.3462 Evaluate side-chains 24 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 23 optimal weight: 0.7980 chunk 21 optimal weight: 0.0980 chunk 11 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 25 optimal weight: 0.4980 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.131034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.116853 restraints weight = 3022.954| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.73 r_work: 0.3229 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.0774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2199 Z= 0.133 Angle : 0.468 5.150 3015 Z= 0.258 Chirality : 0.038 0.115 372 Planarity : 0.003 0.032 359 Dihedral : 4.179 16.730 310 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 3.70 % Allowed : 6.48 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.52), residues: 277 helix: 2.31 (0.35), residues: 222 sheet: None (None), residues: 0 loop : -1.75 (0.79), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 173 HIS 0.003 0.001 HIS R 178 PHE 0.010 0.001 PHE R 282 TYR 0.006 0.001 TYR R 308 ARG 0.002 0.000 ARG R 175 Details of bonding type rmsd hydrogen bonds : bond 0.06113 ( 163) hydrogen bonds : angle 4.14260 ( 486) SS BOND : bond 0.00205 ( 1) SS BOND : angle 0.18729 ( 2) covalent geometry : bond 0.00270 ( 2198) covalent geometry : angle 0.46845 ( 3013) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.210 Fit side-chains REVERT: R 334 ILE cc_start: 0.8346 (OUTLIER) cc_final: 0.8081 (mp) outliers start: 8 outliers final: 4 residues processed: 31 average time/residue: 0.1741 time to fit residues: 6.2623 Evaluate side-chains 28 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 334 ILE Chi-restraints excluded: chain R residue 340 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 17 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 3 optimal weight: 0.2980 chunk 1 optimal weight: 0.7980 chunk 10 optimal weight: 0.0980 chunk 26 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 178 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.132694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.117629 restraints weight = 2974.135| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.75 r_work: 0.3251 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2199 Z= 0.129 Angle : 0.463 5.125 3015 Z= 0.256 Chirality : 0.038 0.112 372 Planarity : 0.003 0.026 359 Dihedral : 4.174 16.744 310 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.24 % Allowed : 12.96 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.51), residues: 277 helix: 2.39 (0.34), residues: 222 sheet: None (None), residues: 0 loop : -1.82 (0.80), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 173 HIS 0.005 0.002 HIS R 178 PHE 0.011 0.001 PHE R 282 TYR 0.006 0.001 TYR R 308 ARG 0.003 0.001 ARG R 175 Details of bonding type rmsd hydrogen bonds : bond 0.05959 ( 163) hydrogen bonds : angle 3.91938 ( 486) SS BOND : bond 0.00183 ( 1) SS BOND : angle 0.20810 ( 2) covalent geometry : bond 0.00266 ( 2198) covalent geometry : angle 0.46292 ( 3013) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 22 time to evaluate : 0.206 Fit side-chains revert: symmetry clash REVERT: R 334 ILE cc_start: 0.8346 (OUTLIER) cc_final: 0.8102 (mp) outliers start: 7 outliers final: 3 residues processed: 28 average time/residue: 0.1835 time to fit residues: 5.9797 Evaluate side-chains 26 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 334 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 9 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 0.0980 chunk 25 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 17 optimal weight: 0.0870 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS R 312 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.134125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.118839 restraints weight = 2924.536| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.79 r_work: 0.3254 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2199 Z= 0.115 Angle : 0.441 5.090 3015 Z= 0.244 Chirality : 0.038 0.110 372 Planarity : 0.003 0.027 359 Dihedral : 4.064 16.712 310 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.39 % Allowed : 16.20 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.51), residues: 277 helix: 2.54 (0.34), residues: 222 sheet: None (None), residues: 0 loop : -1.86 (0.79), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 173 HIS 0.002 0.001 HIS R 178 PHE 0.009 0.001 PHE R 282 TYR 0.006 0.001 TYR R 308 ARG 0.004 0.001 ARG R 175 Details of bonding type rmsd hydrogen bonds : bond 0.05411 ( 163) hydrogen bonds : angle 3.77395 ( 486) SS BOND : bond 0.00116 ( 1) SS BOND : angle 0.19541 ( 2) covalent geometry : bond 0.00225 ( 2198) covalent geometry : angle 0.44116 ( 3013) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.235 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 24 average time/residue: 0.2144 time to fit residues: 5.9590 Evaluate side-chains 22 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 7 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 14 optimal weight: 0.3980 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 13 optimal weight: 0.0050 chunk 24 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.131007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.117010 restraints weight = 3068.804| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.70 r_work: 0.3226 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2199 Z= 0.121 Angle : 0.452 5.119 3015 Z= 0.248 Chirality : 0.038 0.109 372 Planarity : 0.003 0.026 359 Dihedral : 4.029 16.618 310 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.31 % Allowed : 16.20 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.58 (0.51), residues: 277 helix: 2.52 (0.34), residues: 222 sheet: None (None), residues: 0 loop : -1.90 (0.79), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 109 HIS 0.002 0.001 HIS R 93 PHE 0.009 0.001 PHE R 282 TYR 0.006 0.001 TYR R 308 ARG 0.004 0.001 ARG R 175 Details of bonding type rmsd hydrogen bonds : bond 0.05573 ( 163) hydrogen bonds : angle 3.84575 ( 486) SS BOND : bond 0.00138 ( 1) SS BOND : angle 0.19688 ( 2) covalent geometry : bond 0.00249 ( 2198) covalent geometry : angle 0.45229 ( 3013) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: R 72 ILE cc_start: 0.8007 (OUTLIER) cc_final: 0.7769 (mp) outliers start: 5 outliers final: 3 residues processed: 26 average time/residue: 0.1975 time to fit residues: 5.9878 Evaluate side-chains 25 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 72 ILE Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 2 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 6 optimal weight: 0.0010 chunk 20 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.128396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.114283 restraints weight = 3093.975| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.72 r_work: 0.3190 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2199 Z= 0.139 Angle : 0.468 5.156 3015 Z= 0.258 Chirality : 0.039 0.111 372 Planarity : 0.003 0.026 359 Dihedral : 4.169 16.502 310 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.31 % Allowed : 16.20 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.51), residues: 277 helix: 2.45 (0.34), residues: 222 sheet: None (None), residues: 0 loop : -1.93 (0.79), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 99 HIS 0.003 0.001 HIS R 93 PHE 0.011 0.001 PHE R 282 TYR 0.007 0.001 TYR R 308 ARG 0.004 0.001 ARG R 175 Details of bonding type rmsd hydrogen bonds : bond 0.06166 ( 163) hydrogen bonds : angle 3.89041 ( 486) SS BOND : bond 0.00203 ( 1) SS BOND : angle 0.21395 ( 2) covalent geometry : bond 0.00301 ( 2198) covalent geometry : angle 0.46828 ( 3013) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: R 72 ILE cc_start: 0.8048 (OUTLIER) cc_final: 0.7803 (mp) outliers start: 5 outliers final: 3 residues processed: 27 average time/residue: 0.1949 time to fit residues: 6.0797 Evaluate side-chains 26 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 72 ILE Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 11 optimal weight: 0.0070 chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 0.0470 chunk 15 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.129436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.114498 restraints weight = 3132.788| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.91 r_work: 0.3187 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2199 Z= 0.125 Angle : 0.450 5.098 3015 Z= 0.248 Chirality : 0.038 0.109 372 Planarity : 0.003 0.025 359 Dihedral : 4.100 16.763 310 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.31 % Allowed : 17.59 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.51), residues: 277 helix: 2.51 (0.34), residues: 222 sheet: None (None), residues: 0 loop : -1.91 (0.81), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 99 HIS 0.002 0.001 HIS R 93 PHE 0.010 0.001 PHE R 282 TYR 0.007 0.001 TYR R 308 ARG 0.005 0.001 ARG R 175 Details of bonding type rmsd hydrogen bonds : bond 0.05800 ( 163) hydrogen bonds : angle 3.81391 ( 486) SS BOND : bond 0.00146 ( 1) SS BOND : angle 0.21957 ( 2) covalent geometry : bond 0.00259 ( 2198) covalent geometry : angle 0.44996 ( 3013) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: R 72 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7785 (mp) REVERT: R 334 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.8122 (mp) outliers start: 5 outliers final: 3 residues processed: 25 average time/residue: 0.2096 time to fit residues: 6.0693 Evaluate side-chains 25 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 72 ILE Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 334 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 13 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.126049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.111180 restraints weight = 3180.006| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.91 r_work: 0.3142 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2199 Z= 0.159 Angle : 0.487 5.198 3015 Z= 0.271 Chirality : 0.040 0.113 372 Planarity : 0.003 0.026 359 Dihedral : 4.250 16.622 310 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.31 % Allowed : 17.59 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.51), residues: 277 helix: 2.33 (0.34), residues: 222 sheet: None (None), residues: 0 loop : -1.88 (0.82), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 99 HIS 0.003 0.001 HIS R 93 PHE 0.011 0.001 PHE R 282 TYR 0.007 0.001 TYR R 308 ARG 0.005 0.001 ARG R 175 Details of bonding type rmsd hydrogen bonds : bond 0.06752 ( 163) hydrogen bonds : angle 3.97818 ( 486) SS BOND : bond 0.00285 ( 1) SS BOND : angle 0.26237 ( 2) covalent geometry : bond 0.00357 ( 2198) covalent geometry : angle 0.48734 ( 3013) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: R 72 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7854 (mp) outliers start: 5 outliers final: 3 residues processed: 29 average time/residue: 0.1812 time to fit residues: 6.1060 Evaluate side-chains 27 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 72 ILE Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 21 optimal weight: 0.0170 chunk 7 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.127954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.113771 restraints weight = 3137.795| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.73 r_work: 0.3181 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2199 Z= 0.137 Angle : 0.468 5.089 3015 Z= 0.262 Chirality : 0.038 0.109 372 Planarity : 0.003 0.026 359 Dihedral : 4.179 16.959 310 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.85 % Allowed : 18.52 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.51), residues: 277 helix: 2.34 (0.34), residues: 222 sheet: None (None), residues: 0 loop : -1.80 (0.82), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 173 HIS 0.003 0.001 HIS R 93 PHE 0.010 0.001 PHE R 282 TYR 0.007 0.001 TYR R 308 ARG 0.004 0.001 ARG R 175 Details of bonding type rmsd hydrogen bonds : bond 0.06162 ( 163) hydrogen bonds : angle 3.96142 ( 486) SS BOND : bond 0.00176 ( 1) SS BOND : angle 0.23320 ( 2) covalent geometry : bond 0.00290 ( 2198) covalent geometry : angle 0.46834 ( 3013) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: R 72 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7823 (mp) outliers start: 4 outliers final: 3 residues processed: 25 average time/residue: 0.2014 time to fit residues: 5.8316 Evaluate side-chains 25 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 72 ILE Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 5 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.127454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.113236 restraints weight = 3134.835| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.75 r_work: 0.3176 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2199 Z= 0.141 Angle : 0.474 5.110 3015 Z= 0.264 Chirality : 0.039 0.111 372 Planarity : 0.003 0.026 359 Dihedral : 4.185 16.818 310 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.85 % Allowed : 18.98 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.51), residues: 277 helix: 2.31 (0.34), residues: 222 sheet: None (None), residues: 0 loop : -1.75 (0.85), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 173 HIS 0.003 0.001 HIS R 93 PHE 0.011 0.001 PHE R 282 TYR 0.009 0.001 TYR R 185 ARG 0.006 0.001 ARG R 175 Details of bonding type rmsd hydrogen bonds : bond 0.06262 ( 163) hydrogen bonds : angle 3.94625 ( 486) SS BOND : bond 0.00195 ( 1) SS BOND : angle 0.23668 ( 2) covalent geometry : bond 0.00309 ( 2198) covalent geometry : angle 0.47400 ( 3013) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: R 72 ILE cc_start: 0.8037 (OUTLIER) cc_final: 0.7756 (mp) outliers start: 4 outliers final: 3 residues processed: 26 average time/residue: 0.1961 time to fit residues: 5.9220 Evaluate side-chains 26 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 72 ILE Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 5 optimal weight: 0.4980 chunk 14 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.127739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.112948 restraints weight = 3102.112| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.89 r_work: 0.3169 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2199 Z= 0.138 Angle : 0.470 5.101 3015 Z= 0.262 Chirality : 0.038 0.109 372 Planarity : 0.003 0.027 359 Dihedral : 4.173 16.829 310 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.85 % Allowed : 18.98 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.52), residues: 277 helix: 2.32 (0.34), residues: 222 sheet: None (None), residues: 0 loop : -1.64 (0.88), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 173 HIS 0.003 0.001 HIS R 93 PHE 0.011 0.001 PHE R 282 TYR 0.017 0.001 TYR R 185 ARG 0.005 0.001 ARG R 175 Details of bonding type rmsd hydrogen bonds : bond 0.06203 ( 163) hydrogen bonds : angle 3.92576 ( 486) SS BOND : bond 0.00182 ( 1) SS BOND : angle 0.23074 ( 2) covalent geometry : bond 0.00299 ( 2198) covalent geometry : angle 0.46966 ( 3013) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1541.28 seconds wall clock time: 27 minutes 40.81 seconds (1660.81 seconds total)